I created a customization for a red and green changing Christmas light. When directly applying this customization to a bulb everything works well. When using it as part of a scene nothing happens. The only way is to first apply the customization and then use the current state for the scene but this looks way worse and is unpreferable.
I was having the same problem when I first created a scene with a custom flow. Then I created a second scene with a favourite white and when I activated that I could then go back to the Custom scene, try that and see how it goes